Background: 16S ribosomal RNA (rRNA) and 18S rRNA gene polymerase chain reaction (16/18S PCR) with sequencing can provide expeditious bacterial or fungal pathogen identification from sterile site samples (cost $474/PCR). Our objective was to assess the utilization and diagnostic yield of 16/18S PCR of sterile site samples in pediatric patients.
Methods: Patients sterile site fluid or direct tissue specimens were collected and cultured at Lurie Childrens Hospital of Chicago and sent to Northwestern Memorial Hospital for 16/18S PCR as clinically indicated. Clinical data were reviewed including PCRs, cultures, and medical conditions.
Results: 16/18S PCR testing increased over the study period. In total, 177 samples were sent for 16S and/or 18S PCR from 146 patients (1/2016-4/2018). Osteoarticular, CSF, pleural fluid and organ tissue (n=28; lung=19, chest mass=2, liver=2, spleen=2, etc.) sites were most frequent. Yield of 16/18S PCR by source is listed in Table 1. Twenty-eight of 156 samples for 16S PCR were positive (17.9%); 21 with a single organism ID, 1 with two organisms, and 6 indeterminate. (Table 2). Of negative 16S PCR samples, 1 grew Mycobacterium avium complex in culture. 18S PCR was performed on 108 unique samples; 7 were positive (6.5%, Table 3). For 4 positive 18S PCRs, a fungus also grew in culture with 3 concordant results and 1 discordant. Two negative 18S PCR samples grew molds (Phellinus spp.; Blastomyces dermatitidis). All patients (100%) with positive 18S PCR were immunocompromised compared to 21% (6/28) with positive 16S PCR. Both 16S and 18S PCRs were sent on 87 samples of which 16S PCR was positive in 5, 18S PCR was positive in 3, and none had both 16/18S PCRs positive.
Conclusion: 16/18S PCR can provide important infectious pathogen diagnostics. 16S PCR should be sent only if bacterial culture is negative with higher yield sites being brain, abscess, pleural effusion, bone/joint and CSF. 16S PCR appears useful if an anaerobic pathogen is likely but conditions are not optimal for recovery. 18S PCR is highest yield in patients at risk of fungal disease. 16 and 18S PCRs were often sent together, likely reflexively. Selective or sequential testing may be advisable for most cases, guided by clinical index of suspicion. Best practices to optimize resource utilization and clinical impact are evolving.
L. B. Mithal,
M. Malczynski, None
P. C. Seed, None